Frequently Asked Questions

How do I obtain individual-level data?
Each project has its own information on how and where individual-level data can be obtained. Please see the Project Description tab for specifics on data for that project.

How do I cite data from this site?
See the Data Usage page for detailed citation instructions and guidelines.

Where is the X-chromosome in the Genes and Interactions Controlling Oral Clefts data?
The data for this project is limited to autosomes.

Why is there no Manhattan Plot for the options I selected?
If the data has an insufficient sample size (e.g., number of trios) for the analysis, no plot will be displayed.

Why is the Interactive Manhattan Plot going so slowly?
The software used to generate the dynamic plots can take a while to plot each data point, especially for larger chromosomes. It is web browser dependent - make sure you are using the most recent and up-to-date version of your preferred browser. Microsoft Edge works fastest on Windows machines, Safari on Macs. We also recommend you only have one tab open at a time. Please click the submit button only once and be patient - you will get a plot in a few moments.

How do I use the Interactive Manhattan Plot?
When you first make your selection, the plot will open in a new tab. The top of the page will show a static plot of all chromosomes and the options you selected on the data form. Below that plot is a box for Chromosome. Select the chromosome from the drop-down menu and click the Update Plot button. The software will then render a plot based on that selection. Note: larger chromosomes will take longer to plot.

Once the interactive plot image appears you can then scroll left or right, zoom in or out, zoom in a specific area, hover over points for more information, and download the current view of the plot as a .png file. All of the interactive options appear to the upper right of the plot when you hover over it.

How do I use Locus Zoom?

  • Explore different regions in the genome in a variety of different ways:
    • Click and drag the plot to pan left/right
    • Shift+Scroll the mousewheel to zoom in or out
    • Click and drag x-axis or y-axis ticks to scale that axis
    • Shift+click and drag x-axis or y-axis ticks to pan along that axis
    • Use the Pan / Zoom Region buttons to navigate around the currently shown region
    • Use the Show Region By Gene dropdown to jump to regions centered around preselected genes
    • Enter an arbitrary region in the Show Specific Region input using the format chr:start-end (e.g. 16:53519169-54119169)
  • Click on genes or variants in any part of the plot for more information about them
  • Use the + ADD STUDY and + ADD BED TRACK buttons to browse available data sets and add them to the plot.
  • Remove analyses from the plot using the X button that appears when your mouse is over the panel for that analysis.

Help!
If you are having any other problems, questions, or concerns, please contact our Help Desk.